Contacts of the helix formed by residues 263 - 274 (chain H) in PDB entry 3U3F
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 263 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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921D ILE* 4.6 9.9 - - + -
925D ASP* 4.6 7.3 + - - +
943D GLN* 4.5 32.3 - - + +
944D LYS* 5.7 1.8 - - - +
947D ASN* 3.3 18.9 + - - +
262H SER* 1.3 75.9 - - - +
264H THR* 1.3 64.2 + - - +
266H GLU* 3.0 16.9 + - - +
267H LEU* 3.0 8.9 + - - -
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Residues in contact with THR 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918D ARG* 5.5 11.0 - - + +
921D ILE* 4.1 16.3 - - + +
922D GLY* 5.6 5.2 - - - -
925D ASP* 4.0 18.8 - - + +
262H SER 3.5 10.9 + - - -
263H ALA* 1.3 72.1 - - - +
265H ARG* 1.3 58.9 + - - +
267H LEU* 2.8 13.5 + - + +
268H ASP* 2.6 50.3 + - - +
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Residues in contact with ARG 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262H SER* 2.7 20.0 + - - +
264H THR* 1.3 76.1 + - - +
266H GLU* 1.3 62.9 + - - +
268H ASP* 3.8 5.7 - - - +
269H GLU* 2.9 26.9 + - - +
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Residues in contact with GLU 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944D LYS* 6.2 3.6 - - + -
947D ASN* 4.1 14.1 - - + +
262H SER 3.6 2.7 + - - +
263H ALA* 3.0 11.2 + - - +
265H ARG* 1.3 77.8 - - - +
267H LEU* 1.3 63.0 + - - +
269H GLU* 3.7 6.0 - - - +
270H LEU* 3.3 25.6 + - + +
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Residues in contact with LEU 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914D GLY 4.8 2.7 - - - +
917D LEU* 3.8 11.9 - - + -
918D ARG* 3.4 50.5 - - + +
921D ILE* 4.2 10.3 - - + -
947D ASN* 3.6 23.9 - - - +
950D LEU* 3.3 33.9 - - + -
263H ALA 3.0 9.6 + - - +
264H THR* 2.8 14.1 + - - +
266H GLU* 1.3 74.0 - - - +
268H ASP* 1.3 52.9 + - - +
269H GLU 3.0 4.0 - - - -
270H LEU* 2.9 12.5 + - + +
271H MET* 2.7 39.7 + - + +
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Residues in contact with ASP 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886B GLU* 5.6 0.3 - - - +
919B LYS* 5.0 3.5 + - - -
918D ARG* 3.1 39.0 + - - -
264H THR* 2.6 38.2 + - - +
265H ARG* 4.1 5.2 + - - +
267H LEU* 1.3 72.2 - - - +
269H GLU* 1.3 53.7 + - - +
271H MET* 3.4 12.7 - - - +
272H ALA* 2.8 32.2 + - - +
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Residues in contact with GLU 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265H ARG 2.9 18.9 + - - +
266H GLU* 3.7 7.6 - - - +
268H ASP* 1.3 74.9 - - - +
270H LEU* 1.3 65.2 + - - +
272H ALA* 3.2 15.4 + - - +
273H SER* 3.2 14.0 + - - -
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Residues in contact with LEU 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947D ASN* 3.4 37.9 - - + +
950D LEU* 4.6 10.3 - - + -
951D ALA* 3.4 33.7 - - + +
954D ILE* 4.0 18.6 - - + +
955D ASN* 6.1 0.7 - - - +
266H GLU* 3.3 17.0 + - + +
267H LEU* 2.9 10.0 + - - +
269H GLU* 1.3 77.0 - - - +
271H MET* 1.3 63.6 + - - +
273H SER* 2.6 26.5 + - - +
274H LEU* 3.6 7.6 + - - +
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Residues in contact with MET 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911D LYS* 3.1 38.1 - - + +
914D GLY* 3.5 16.4 - - - +
915D LEU* 3.3 30.3 - - + +
918D ARG* 5.8 3.8 - - + -
950D LEU* 4.7 9.0 - - - -
267H LEU* 2.7 24.0 + - + +
268H ASP* 3.4 19.1 - - - +
270H LEU* 1.3 72.2 - - - +
272H ALA* 1.3 62.9 + - - +
274H LEU* 3.0 45.2 + - + +
275H SER* 4.2 0.7 + - - -
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Residues in contact with ALA 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268H ASP 2.8 22.1 + - - +
269H GLU* 3.2 10.5 + - - +
271H MET* 1.3 72.3 - - - +
273H SER* 1.3 56.4 + - - +
275H SER* 3.0 30.6 + - - -
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Residues in contact with SER 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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954D ILE* 4.9 9.4 - - - +
958D ARG* 3.1 17.6 + - - -
269H GLU 3.2 6.9 + - - -
270H LEU* 2.6 25.6 + - - +
272H ALA* 1.3 76.8 - - - +
274H LEU* 1.3 59.8 + - - +
275H SER 3.1 4.7 + - - -
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Residues in contact with LEU 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907D VAL* 4.0 21.5 - - + +
910D VAL* 4.6 6.3 - - + +
911D LYS* 4.1 30.3 - - + +
914D GLY* 5.6 0.2 - - - -
950D LEU* 5.9 0.9 - - + -
954D ILE* 3.6 40.6 - - + -
957D MET* 3.8 17.7 - - + -
958D ARG* 3.5 12.7 + - - +
270H LEU 3.9 5.8 - - - +
271H MET* 3.0 52.9 + - + +
273H SER* 1.3 77.4 + - - +
275H SER* 1.3 64.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il